Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis

Abstract

BackgroundWorldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.ResultsMore than 25 million short reads generated by the Illumina Genome Analyzer were de novo assembled in 22,761 contigs with an average size of 260 bp. With a stringent E-value threshold of 10-10, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.ConclusionThis data represents the most comprehensive genomic resource for the South African abalone H. midae to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in H. midae and in other abalone species.

De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae

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Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

“…A/G and C/T were the most frequent SNP types observed while the G/T and G/C were the least common types. These findings are in line with the previous SNP studies based on transcriptome datasets in a number of aquatic species (Franchini et al, 2011;Jung et al, 2011;Wang et al, 2013;Cui et al, 2014).…”

De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima

“…These unigene sequences are similar to reports for P. martensii (mean length of unigene: 393 8) and 434 bp 12) ) and P. maxima (447 bp 16) ). The sequences obtained were larger than that of H. midae (260 bp 24) ). Given the lack of a reference genome, estimating the number of genes and predicting the potential functions of the transcripts were difficult.…”